data_2P05 # _model_server_result.job_id 6jVZITcBfhDNz6VRZqkYXQ _model_server_result.datetime_utc '2025-08-31 20:31:39' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2p05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":100}' # _entry.id 2P05 # _exptl.entry_id 2P05 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2P05 _cell.length_a 71.46 _cell.length_b 71.46 _cell.length_c 55.26 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 55.26 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 25 A CYS 23 1_555 B ZN ZN . A ZN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A SG CYS 28 A CYS 26 1_555 B ZN ZN . A ZN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 A SG CYS 48 A CYS 46 1_555 B ZN ZN . A ZN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc4 A SG CYS 51 A CYS 49 1_555 B ZN ZN . A ZN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 38 n n PB O2B ADP sing 39 n n PB O3B ADP sing 40 n n PB O3A ADP sing 41 n n O2B HOB2 ADP sing 42 n n O3B HOB3 ADP sing 43 n n PA O1A ADP doub 44 n n PA O2A ADP sing 45 n n PA O3A ADP sing 46 n n PA O5' ADP sing 47 n n O2A HOA2 ADP sing 48 n n O5' C5' ADP sing 49 n n C5' C4' ADP sing 50 n n C5' "H5'1" ADP sing 51 n n C5' "H5'2" ADP sing 52 n n C4' O4' ADP sing 53 n n C4' C3' ADP sing 54 n n C4' H4' ADP sing 55 n n O4' C1' ADP sing 56 n n C3' O3' ADP sing 57 n n C3' C2' ADP sing 58 n n C3' H3' ADP sing 59 n n O3' HO3' ADP sing 60 n n C2' O2' ADP sing 61 n n C2' C1' ADP sing 62 n n C2' H2' ADP sing 63 n n O2' HO2' ADP sing 64 n n C1' N9 ADP sing 65 n n C1' H1' ADP sing 66 n n N9 C8 ADP sing 67 n y N9 C4 ADP sing 68 n y C8 N7 ADP doub 69 n y C8 H8 ADP sing 70 n n N7 C5 ADP sing 71 n y C5 C6 ADP sing 72 n y C5 C4 ADP doub 73 n y C6 N6 ADP sing 74 n n C6 N1 ADP doub 75 n y N6 HN61 ADP sing 76 n n N6 HN62 ADP sing 77 n n N1 C2 ADP sing 78 n y C2 N3 ADP doub 79 n y C2 H2 ADP sing 80 n n N3 C4 ADP sing 81 n y # _atom_sites.entry_id 2P05 _atom_sites.fract_transf_matrix[1][1] 0.013994 _atom_sites.fract_transf_matrix[1][2] 0.008079 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016159 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018096 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ZN A 1 200 200 ZN ZN . C 3 CL A 1 300 300 CL CL . D 4 ADP A 1 100 100 ADP ADP . E 5 1PE A 1 400 400 1PE 1PE . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . D 4 -1.373 25.619 18.754 1 62.64 ? PB ADP 100 A 1 HETATM 2 O O1B ADP . . . D 4 -1.146 24.966 17.383 1 63.11 ? O1B ADP 100 A 1 HETATM 3 O O2B ADP . . . D 4 -2.63 26.5 18.865 1 60.84 ? O2B ADP 100 A 1 HETATM 4 O O3B ADP . . . D 4 -1.06 24.749 19.982 1 61.27 ? O3B ADP 100 A 1 HETATM 5 P PA ADP . . . D 4 -0.221 28.119 18.668 1 50.64 ? PA ADP 100 A 1 HETATM 6 O O1A ADP . . . D 4 1.118 28.513 19.261 1 49.48 ? O1A ADP 100 A 1 HETATM 7 O O2A ADP . . . D 4 -1.569 28.461 19.295 1 50.36 ? O2A ADP 100 A 1 HETATM 8 O O3A ADP . . . D 4 -0.066 26.549 18.676 1 56.29 ? O3A ADP 100 A 1 HETATM 9 O O5' ADP . . . D 4 -0.289 28.506 17.1 1 47 ? O5' ADP 100 A 1 HETATM 10 C C5' ADP . . . D 4 0.632 27.905 16.195 1 41.48 ? C5' ADP 100 A 1 HETATM 11 C C4' ADP . . . D 4 1.085 28.801 15.038 1 35.5 ? C4' ADP 100 A 1 HETATM 12 O O4' ADP . . . D 4 0.645 30.141 15.195 1 30.6 ? O4' ADP 100 A 1 HETATM 13 C C3' ADP . . . D 4 2.596 28.836 15.101 1 35.57 ? C3' ADP 100 A 1 HETATM 14 O O3' ADP . . . D 4 3.232 28.8 13.813 1 37.12 ? O3' ADP 100 A 1 HETATM 15 C C2' ADP . . . D 4 2.827 30.147 15.79 1 33.37 ? C2' ADP 100 A 1 HETATM 16 O O2' ADP . . . D 4 4.082 30.724 15.489 1 36.65 ? O2' ADP 100 A 1 HETATM 17 C C1' ADP . . . D 4 1.779 31.004 15.174 1 29.97 ? C1' ADP 100 A 1 HETATM 18 N N9 ADP . . . D 4 1.655 32.202 16.043 1 29.71 ? N9 ADP 100 A 1 HETATM 19 C C8 ADP . . . D 4 0.63 32.395 16.888 1 28.13 ? C8 ADP 100 A 1 HETATM 20 N N7 ADP . . . D 4 0.774 33.568 17.543 1 28.4 ? N7 ADP 100 A 1 HETATM 21 C C5 ADP . . . D 4 1.901 34.136 17.142 1 27.29 ? C5 ADP 100 A 1 HETATM 22 C C6 ADP . . . D 4 2.562 35.392 17.481 1 28.17 ? C6 ADP 100 A 1 HETATM 23 N N6 ADP . . . D 4 1.961 36.181 18.407 1 27.94 ? N6 ADP 100 A 1 HETATM 24 N N1 ADP . . . D 4 3.736 35.669 16.861 1 28.4 ? N1 ADP 100 A 1 HETATM 25 C C2 ADP . . . D 4 4.255 34.806 15.949 1 28.3 ? C2 ADP 100 A 1 HETATM 26 N N3 ADP . . . D 4 3.679 33.64 15.594 1 27.28 ? N3 ADP 100 A 1 HETATM 27 C C4 ADP . . . D 4 2.504 33.251 16.148 1 28.03 ? C4 ADP 100 A 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #